Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold999
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51679
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:15188 original size:13 final size:13
Alignment explanation
Indices: 15170--15194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15160 AGCTTGCACA
15170 GTATCGATACATT
1 GTATCGATACATT
15183 GTATCGATACAT
1 GTATCGATACAT
15195 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:15207 original size:20 final size:21
Alignment explanation
Indices: 15182--15231 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
15172 ATCGATACAT
**
15182 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
15202 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
15223 TGTATCGAT
1 TGTATCGAT
15232 TCAGGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:15309 original size:20 final size:20
Alignment explanation
Indices: 15268--15319 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
15258 TAGCCAAATT
*
15268 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
15287 TGTATCGATACATCACAAAA
1 TGTATCGATACATCACAAAA
15307 TGTATCGATACAT
1 TGTATCGATACAT
15320 TGGCTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:21258 original size:8 final size:8
Alignment explanation
Indices: 21245--21270 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21235 ATTTGATTCA
21245 ATTTTGTG
1 ATTTTGTG
21253 ATTTTGTG
1 ATTTTGTG
21261 ATTTTGTG
1 ATTTTGTG
21269 AT
1 AT
21271 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:21493 original size:13 final size:13
Alignment explanation
Indices: 21475--21536 Score: 106
Period size: 13 Copynumber: 4.8 Consensus size: 13
21465 GCATTCTCTA
*
21475 TATCGATACATTG
1 TATCGATACAGTG
21488 TATCGATACAGTG
1 TATCGATACAGTG
*
21501 TATCGATACATTG
1 TATCGATACAGTG
21514 TATCGATACAGTG
1 TATCGATACAGTG
21527 TATCGATACA
1 TATCGATACA
21537 AAGGGTTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:21511 original size:26 final size:26
Alignment explanation
Indices: 21475--21536 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
21465 GCATTCTCTA
21475 TATCGATACATTGTATCGATACAGTG
1 TATCGATACATTGTATCGATACAGTG
21501 TATCGATACATTGTATCGATACAGTG
1 TATCGATACATTGTATCGATACAGTG
21527 TATCGATACA
1 TATCGATACA
21537 AAGGGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (26 bp):
TATCGATACATTGTATCGATACAGTG
Found at i:24009 original size:13 final size:13
Alignment explanation
Indices: 23991--24015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23981 AGCTTGCACA
23991 GTATCGATACATT
1 GTATCGATACATT
24004 GTATCGATACAT
1 GTATCGATACAT
24016 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:24028 original size:20 final size:21
Alignment explanation
Indices: 24003--24055 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
23993 ATCGATACAT
*
24003 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
24023 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
24044 TGTATCGATACA
1 TGTATCGATACA
24056 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:24130 original size:20 final size:20
Alignment explanation
Indices: 24089--24140 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
24079 TAGCCAAATT
*
24089 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
24108 TGTATCGATACATCACAAAA
1 TGTATCGATACATCACAAAA
24128 TGTATCGATACAT
1 TGTATCGATACAT
24141 TGGCTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:35916 original size:14 final size:14
Alignment explanation
Indices: 35899--35932 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
35889 TGTTAATTAT
35899 TTTTAATTTTTTAG
1 TTTTAATTTTTTAG
*
35913 TTTTAATTTTTTAT
1 TTTTAATTTTTTAG
35927 TTTTAA
1 TTTTAA
35933 ATGATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTAATTTTTTAG
Found at i:37050 original size:22 final size:21
Alignment explanation
Indices: 37005--37051 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
36995 AATTACAGAA
*
37005 AAAAAAAAATAAAAATATATT
1 AAAAAAAAATAAAAATATAAT
* *
37026 AAAAAAAAATACAACATTTAAT
1 AAAAAAAAATA-AAAATATAAT
37048 AAAA
1 AAAA
37052 TTTAAAACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAAAAATAAAAATATAAT
Found at i:37362 original size:29 final size:32
Alignment explanation
Indices: 37301--37367 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
37291 AAAATATTTT
*
37301 TTATATAAATTTTGATAAATAAATAATTTATA
1 TTATATAAATTTTGATAAATAAATAATATATA
* *
37333 TTATATAAATTTT-A-AAAT-ATTTATATATA
1 TTATATAAATTTTGATAAATAAATAATATATA
37362 TTATAT
1 TTATAT
37368 TTTTATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.44
30 4 0.12
31 1 0.03
32 13 0.41
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
TTATATAAATTTTGATAAATAAATAATATATA
Found at i:38740 original size:16 final size:15
Alignment explanation
Indices: 38712--38758 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
38702 TAAGTATTTA
38712 AAATTTTATATAATAT
1 AAATTTTATATAA-AT
38728 AAATTATTA-ATAAAT
1 AAATT-TTATATAAAT
*
38743 AAATTTTATAAAAAT
1 AAATTTTATATAAAT
38758 A
1 A
38759 TGTTAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 13 0.46
16 9 0.32
17 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTTTATATAAAT
Found at i:38746 original size:15 final size:16
Alignment explanation
Indices: 38712--38752 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
38702 TAAGTATTTA
38712 AAATTTTATATAATAT
1 AAATTTTATATAATAT
38728 AAATTATTA-ATAA-AT
1 AAATT-TTATATAATAT
38743 AAATTTTATA
1 AAATTTTATA
38753 AAAATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 8 0.35
16 9 0.39
17 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTTATATAATAT
Found at i:44253 original size:18 final size:18
Alignment explanation
Indices: 44230--44321 Score: 81
Period size: 17 Copynumber: 5.4 Consensus size: 18
44220 AAAAATTATT
44230 AAATATTATATAATATAA
1 AAATATTATATAATATAA
*
44248 AAATA-TATA-AATATTTA
1 AAATATTATATAATA-TAA
*
44265 AAATTTTATATAATAT-A
1 AAATATTATATAATATAA
* *
44282 AATTATTA-AT-ATATTA
1 AAATATTATATAATATAA
44298 AAAT-TTATATAA-ATATA
1 AAATATTATATAATATA-A
44315 AAATATT
1 AAATATT
44322 TAAATTTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.12
16 14 0.23
17 23 0.38
18 12 0.20
19 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATTATATAATATAA
Found at i:44313 original size:33 final size:33
Alignment explanation
Indices: 44226--44321 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
44216 TATAAAAAAT
* *
44226 TATT-AAATATTATATAATATAAAAATATATAAATA
1 TATTAAAAT-TTATATAA-ATATAAAT-TATTAATA
44261 T-TTAAAATTT-TATATAATATAAATTATTAATA
1 TATTAAAATTTATATA-AATATAAATTATTAATA
*
44293 TATTAAAATTTATATAAATATAAAATATT
1 TATTAAAATTTATATAAATATAAATTATT
44322 TAAATTTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
32 8 0.15
33 32 0.59
34 9 0.17
35 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TATTAAAATTTATATAAATATAAATTATTAATA
Found at i:44319 original size:59 final size:58
Alignment explanation
Indices: 44215--44341 Score: 156
Period size: 59 Copynumber: 2.2 Consensus size: 58
44205 TTTAAATACG
*
44215 ATATAA-A-AAATTATTAAATATTATATAATATAAAAATATATAAATATTTAAAATTTT
1 ATATAATATAAATTATTAAATATTATATAATATAAAAATATATAAATATTT-AAATTTA
*
44272 ATATAATATAAATTATTAATATATTA-A-AATTTATATAAATATA-AAATATTTAAATTTA
1 ATATAATATAAATTATTAA-ATATTATATAA--TATAAAAATATATAAATATTTAAATTTA
44330 ATTATAATATAA
1 A-TATAATATAA
44342 TAAAATATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
57 6 0.10
58 10 0.16
59 29 0.47
60 17 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (58 bp):
ATATAATATAAATTATTAAATATTATATAATATAAAAATATATAAATATTTAAATTTA
Found at i:44338 original size:26 final size:25
Alignment explanation
Indices: 44277--44354 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
44267 ATTTTATATA
*
44277 ATATAAATTATTAATATATTAAAATTT
1 ATATAAA-TA-TAAAATATTAAAATTT
*
44304 ATATAAATATAAAATATTTAAATTT
1 ATATAAATATAAAATATTAAAATTT
44329 AATTATAATATAATAAAATATATAAA
1 -A-TATAA-AT-ATAAAATAT-TAAA
44355 TAAAATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 14 0.33
26 3 0.07
27 12 0.28
28 2 0.05
29 9 0.21
30 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATAAATATAAAATATTAAAATTT
Found at i:44443 original size:15 final size:14
Alignment explanation
Indices: 44423--44460 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
44413 AATTATTTTT
44423 TATAAATTTAAATAA
1 TATAAATTTAAAT-A
*
44438 TATAAATTTAGATA
1 TATAAATTTAAATA
44452 T-TAAATTTA
1 TATAAATTTA
44461 TTATTTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 2 0.09
15 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
TATAAATTTAAATA
Found at i:47991 original size:152 final size:151
Alignment explanation
Indices: 47802--48287 Score: 665
Period size: 152 Copynumber: 3.2 Consensus size: 151
47792 TTAGGAGATG
* * *
47802 CCTTAGACGTACAAGTACCTGATA-CTTCTAAAAGACTTAAAAGGATGTGGACGGGGTGAACCTA
1 CCTTCGACGTAAAAGTACCTGATACCCT-TAAAAGACTTAAAAGGATGTGGA-GGGGTGAACCTA
*
47866 TCCTAAATGCCCACCTTCGACATAAAAACGGACCCGGTGACAACCTAAGACTCGATTCTAAGAAA
64 TCCTAAATGCCCACCTTCGGCATAAAAACGGACCCGGTGACAACCTAAGACTCGATTCTAAGAAA
* *
47931 TTACGAAATTACCCTAAGGGATA
129 TTACAAAAATACCCTAAGGGATA
* * *
47954 CCTTCGACGTAAAAGTACCTGATAGCCTTAAAGGACTTAAAAAGGATGTGTATGGGGTG-ACCTA
1 CCTTCGACGTAAAAGTACCTGATACCCTTAAAAGACTT-AAAAGGATGTGGA-GGGGTGAACCTA
* * *
48018 TCCTAAATGCCCACCTTCGGCATAAAAGCGGA-TCGGTGACAACCTAGGACTCGATTCTAAGAAA
64 TCCTAAATGCCCACCTTCGGCATAAAAACGGACCCGGTGACAACCTAAGACTCGATTCTAAGAAA
48082 TTACAAAAATACCCTTAAGGGATA
129 TTACAAAAATACCC-TAAGGGATA
* * * *
48106 CCTTCGACGTGAAAGTATCTGATACCCCTAAAAGACTTAAAAGGATGTGGATGGGTGAACCTATC
1 CCTTCGACGTAAAAGTACCTGATACCCTTAAAAGACTTAAAAGGATGTGGAGGGGTGAACCTATC
* * *
48171 CTAAATGCCCACCTTCGGCATAAAAACGTACCCGGTGACAACCTAAGACTCGATTTTAAAAAATT
66 CTAAATGCCCACCTTCGGCATAAAAACGGACCCGGTGACAACCTAAGACTCGATTCTAAGAAATT
* * *
48236 ATAAAAATACCTCCAAGAGATA
131 ACAAAAATACC-CTAAGGGATA
* *
48258 CCTTTGACGTGAAAA-CACCTGATACCCTTA
1 CCTTCGACGT-AAAAGTACCTGATACCCTTA
48288 GTAGACATTA
Statistics
Matches: 294, Mismatches: 33, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
150 5 0.02
151 89 0.30
152 176 0.60
153 24 0.08
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (151 bp):
CCTTCGACGTAAAAGTACCTGATACCCTTAAAAGACTTAAAAGGATGTGGAGGGGTGAACCTATC
CTAAATGCCCACCTTCGGCATAAAAACGGACCCGGTGACAACCTAAGACTCGATTCTAAGAAATT
ACAAAAATACCCTAAGGGATA
Found at i:50977 original size:18 final size:19
Alignment explanation
Indices: 50943--50978 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
50933 CTCCTGGAAA
*
50943 TGAATTAATTTTTAAAAAC
1 TGAATTAATTATTAAAAAC
50962 TGAATTAA-TATTAAAAA
1 TGAATTAATTATTAAAAA
50979 AATAATGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (19 bp):
TGAATTAATTATTAAAAAC
Found at i:50978 original size:19 final size:19
Alignment explanation
Indices: 50943--50979 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50933 CTCCTGGAAA
* *
50943 TGAATTAATTTTTAAAAAC
1 TGAATTAATATTAAAAAAC
50962 TGAATTAATATTAAAAAA
1 TGAATTAATATTAAAAAA
50980 ATAATGATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
TGAATTAATATTAAAAAAC
Found at i:51016 original size:165 final size:166
Alignment explanation
Indices: 50813--51179 Score: 431
Period size: 166 Copynumber: 2.2 Consensus size: 166
50803 AGTATGAGTT
* * *
50813 AAATAATAATATTTGATAAATTTAAAAAAATAAAAATCAAGAAAAATCC-CT-TAAAAAA-TTAC
1 AAATAATAATATTTGATAAATTTTAAAAATTAAAAATCAAG-AAAATCCTCTCGAAAAAATTTAC
* * * * ** * *
50875 GAAGTAGAAAATATATGTTTTTC-AAAAAAAAAGAAATTTCAAGGAGAAAATTTAAAAA-CTCCT
65 GAAGTAGAAAACATA-ATATTTCGAAAAAAAAA-AAATTTCAA--AAAAAAAATAAAAAGCACAT
* * * *
50938 GGAAATG-AATTAATTTTTAAAAACTGAATTAATATTAAAA
126 GAAAATGAAATGAATTTTTAAAAACTAAATTAATATCAAAA
* * * * *
50978 AAATAATGATGTTTGATGAATTTTGAAAATTGAAAATCAAGAAAATCCTCTCGAAAAAATTTACG
1 AAATAATAATATTTGATAAATTTTAAAAATTAAAAATCAAGAAAATCCTCTCGAAAAAATTTACG
51043 AAGTAGAAAACATAATATTTCGAAAAAAAAAAAATTTCAAAAAAAAAATAAAAAGCACATGAAAA
66 AAGTAGAAAACATAATATTTCGAAAAAAAAAAAATTTCAAAAAAAAAATAAAAAGCACATGAAAA
* * * *
51108 TGAAATGAATTTTTGAAAATTAAATTATTATCAAAT
131 TGAAATGAATTTTTAAAAACTAAATTAATATCAAAA
51144 AAATAATAATATTTGATAAATTTTAAAAATTAAAAA
1 AAATAATAATATTTGATAAATTTTAAAAATTAAAAA
51180 CTAAAAAAAT
Statistics
Matches: 167, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
164 18 0.11
165 45 0.27
166 77 0.46
167 27 0.16
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (166 bp):
AAATAATAATATTTGATAAATTTTAAAAATTAAAAATCAAGAAAATCCTCTCGAAAAAATTTACG
AAGTAGAAAACATAATATTTCGAAAAAAAAAAAATTTCAAAAAAAAAATAAAAAGCACATGAAAA
TGAAATGAATTTTTAAAAACTAAATTAATATCAAAA
Found at i:51084 original size:16 final size:17
Alignment explanation
Indices: 51059--51090 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
51049 AAAACATAAT
51059 ATTTCGAAAAAAAAAAA
1 ATTTCGAAAAAAAAAAA
51076 ATTTC-AAAAAAAAAA
1 ATTTCGAAAAAAAAAA
51091 TAAAAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (17 bp):
ATTTCGAAAAAAAAAAA
Done.